The proteomic core will provide cutting edge discovery protein biochemistry and proteomics tools to address key mechanistic questions, in support ofthe underlying concept that disease-induced changes in autophagy lead to alterations in protein quantity, abundance of specific isoforms and post-translational modifications, which drive cellular phenotype. The core will provide discovery based approaches for protein quantification and the identification of post-translational modifications including phosphorylation, 0-GlcNAcylation and cysteine oxidative modifications for the detailed analysis of a number of subproteomes and protein complexes. The core will employ its recently modified method that allows the site specific quantification and comparison of S-nitrosation, S-glutathionylation and sulfonic acid, the three reversible cysteine modifications. As well, the core will provide multiplex assays for the absolute quantification of key proteins involved in autophagy, lysosomal function, mitochondrial biogenesis and nutrient sensing using multiple reaction monitoring, a targeted mass spectrometry based method. The panels developed will quantify the total protein concentration as well as differentiate between the various protein isoforms which arise from different genes or splice variants of a single gene and for a subset, specific regulatory posttranslational modification.